Exemplar alignment contains indel not found in the overlap indel set

[Jason Walker]

I am seeing the following error message.  Any help would be greatly appreciated.  Let me know what additional details I can provide to help troubleshoot.

ERROR: Exception caught in align_pos() while realigning segment: 1 of read: STARLING_READ id: 1159906 genomic_mapping?: tier1-mapped
full_segment_info:
key: HWI-ST485:138468187:D1Y2NACXX:8:1212:16206:71057/2
id: 1159906
seq:  CACGATGCTATGTTTGTGAGCAACAGACCCATGGGGTTTTCAATCCTGCGAAAGAACTGATTGCTAAACTGGAGAAGTATCGAAAAGCAGAGGGTGGTGC
qual: ?A5@DCCAC@9?9@>;55(;A;>CA;@677C;EHE@GDC;3GIHF:A<FDCGGFD?H@IGHB?>HG?CBD@GHAEFAGEEHE>GHFBH?HHDDDD=D@??
GENOME ALIGNMENT pos: 85759165 strand: R path: 95M1I1N4M
is_realigned? 0
buffer_pos: 0
partial_segment 1 :
GENOME ALIGNMENT pos: 85759165 strand: R path: 95M1I
is_realigned? 0
buffer_pos: 85759165
partial_segment 2 :
GENOME ALIGNMENT pos: 85759261 strand: R path: 4M
is_realigned? 0
buffer_pos: 85759261

FATAL_ERROR: strelka EXCEPTION: ERROR: Exemplar alignment contains indel not found in the overlap indel set
        Indel: INDEL pos: 85759260 type: INSERT len: 1 swap_dlen: 0
Exemplar overlap set:

...caught in main()

[Saunders, Chris]

Hi Jason,

What version of the workflow were you using? I haven't seen this exact error before, but I know that an indel adjacent to an intro like this has been a source of other problems in the past. Would you able to share a slice of the bam file sufficient to reproduce the issue?

Best,

-Chris



________________________________
From: strelka...@googlegroups.com [strelka...@googlegroups.com] on behalf of Jason Walker [jasonw...@gmail.com]
Sent: Tuesday, July 16, 2013 10:15 AM
To: strelka...@googlegroups.com
Subject: [strelka-discuss] Exemplar alignment contains indel not found in the overlap indel set

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[Saunders, Chris]

Hi Jason,

 

I just uploaded strelka_workflow v1.0.10 to the ftp site: https://sites.google.com/site/strelkasomaticvariantcaller/home/download

 

This version should fix the issue described in your email below, and (Sean) disables open-breakend output in the indel vcf file. Please let me know if you’re still experiencing trouble.

 

Best,

 

-Chris

--

[Pascal Gellert]

Hi Chris,

I am using v1.0.14 on RNA-Seq data with GSNAP as aligner. I get a similat error, probably it again has something to do with introns and unmapped regions next to each other. Attached is one of the reads that cause the problem.

Thanks for your help,

Pascal

ERROR: Exception caught in align_pos() while realigning segment: 2 of read: STARLING_READ id: 214725 genomic_mapping?: tier1-mapped

full_segment_info:

key: read314064/F_20818/2

id: 214725

seq:  ATGCGGCCTGAATTCGTGCAGTCTTTGTACACTCAGCTTGACGTACTTTAAGCTGTCTGTAGCTGACCAAAACCACCAAGATGGCAGGAATGCAGCAGAGG

qual: DAEC&FFGF?GGEFFGFDGFFFGEBGFE>GGGFGGFGG9FAGFFEG5GFFGGGGFGFGFFGFEDFEGGGGF>FGGGGGG:GB=GEBEF&GGGGGFGGGGGG

GENOME ALIGNMENT pos: 55587264 strand: R path: 22M3808N51I28M

is_realigned? 0

buffer_pos: 0

partial_segment 1 :

GENOME ALIGNMENT pos: 55587264 strand: R path: 22M

is_realigned? 0

buffer_pos: 55587264

partial_segment 2 :

GENOME ALIGNMENT pos: 55591094 strand: R path: 51I28M

is_realigned? 0

buffer_pos: 55591043

FATAL_ERROR: strelka EXCEPTION: ERROR: Exemplar alignment contains indel not found in the overlap indel set

        Indel: INDEL pos: 55591094 type: INSERT len: 51 swap_dlen: 0

Exemplar overlap set:

INDEL pos: 55591072 type: INSERT len: 3 swap_dlen: 0

status: is_present: 0 is_remove_only: 0

...caught in main()

cmdline: strelka-1.0.14/libexec/strelka2 -clobber -filter-unanchored -min-paired-align-score 20 -min-single-align-score 10 -min-qscore 0 -report-range-begin 50000001 -report-range-end 75000000 -samtools-reference human.fa -max-window-mismatch 3 20 -print-used-allele-counts -bam-seq-name chr10 -genome-size 2858674662 -max-indel-size 50 -indel-nonsite-match-prob 0.5 --min-contig-open-end-support 35 --somatic-snv-rate 0.000001 --shared-site-error-rate 0.0000005 --shared-site-error-strand-bias-fraction 0.5 --somatic-indel-rate 0.000001 --shared-indel-error-rate 0.000001 --tier2-min-single-align-score 5 --tier2-min-paired-align-score 5 --tier2-single-align-score-rescue-mode --tier2-mismatch-density-filter-count 10 --tier2-no-filter-unanchored --tier2-indel-nonsite-match-prob 0.25 --tier2-include-singleton --tier2-include-anomalous -bam-file GSNAP.bam --tumor-bam-file GSNAP_tumor.bam --somatic-snv-file chromosomes/chr10/bins/0002/somatic.snvs.unfiltered.vcf --somatic-indel-file chromosomes/chr10/bins/0002/somatic.indels.unfiltered.vcf --variant-window-flank-file 50 chromosomes/chr10/bins/0002/somatic.indels.unfiltered.vcf.window --max-input-depth 10000 --ignore-conflicting-read-names --report-file chromosomes/chr10/bins/0002/strelka.stats

[Pascal Gellert]

The attachment.

On Tuesday, 16 July 2013 19:15:51 UTC+2, Jason Walker wrote:

[napr]

Were you able to slove the error you mentioned?